DNA microscopy methods

Abstract

The present invention relates to DNA microscopy methods to record the cellular co-localization and / or spatial distributions of arbitrary nucleic acid sequences, or other biomolecules tagged with nucleic sequences. The method involves sequence-components which may identify the targeted sequences-of-interest themselves and / or spatial beacons relative to which their distances are measured.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application is a National Stage application of International Application No. PCT / US2016 / 051164 filed Sep. 9, 2016, which claims the benefit of U.S. Provisional Application No. 62 / 217,639 filed Sep. 11, 2015. The entire contents of the above-identified applications are hereby fully incorporated herein by reference.[0002]The foregoing applications, and all documents cited therein or during their prosecution (“appln cited documents”) and all documents cited or referenced herein (“herein cited documents”), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention. More specifically, all referenced documents are incorporated by reference to the sam...

AI Technical Summary

Benefits of technology

[0014]Advantages of the present invention is that (a) DNA microscopy may work with a single sample, and this sample may be non-canonical and idiosyncratic (such as, but not limited to, tumor tissue, lymphatic tissue or neural tissue); (b) image-capture is volumetric with no sectioning required; (c) the protocol stands alone and does not require specialized equipment; (d) the protocol uses commercialized DNA sequencers to provide high coverage of single template molecules, thereby enabling single-base resolution, low error rates, and high read lengths of gene sequences of interest.

Problems solved by technology

High-throughput sequencing can identify large numbers of heavy- and light-chain variable regions (VH and VL) in a given B-cell repertoire, but information about endogenous pairing of heavy and light chains is lost after bulk lysis of B-cell populations.

RNA sequencing (RNA-Seq) is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification.

The barcodes may be optimized to be unambiguously identifiable, even in the presence of multiple sequencing errors.

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